© Kamla-Raj 2013
Int J Hum Genet, 13(2): 105-111 (2013)
Population Data for 17 Y-STRs in Samples from Southeastern
Anatolia Region of Turkey
Filiz Ozbas-Gerceker*, Nazli Bozman*, Ahmet Arslan# and Ayse Serinδ
*
Department of Biology, Faculty of Arts & Science, University of Gaziantep, Gaziantep, Turkey
#
Department of Medical Biology, Faculty of Medicine, University of Gaziantep,
Gaziantep, Turkey
δ
Cukurova University, Faculty of Medicine, Department of Forensic Medicine, Adana, Turkey
KEYWORDS Y chromosome, Polymorphism, Haplotype, Genetic Distance, Southeastern Anatolia
ABSTRACT In this study, Y chromosome short tandem repeats (Y-STR) haplotype data were obtained for 86 individuals from
the Southeastern Anatolia region of Turkey. Allele frequencies were determined for 17 Y-STRs and haplotypes were obtained.
The highest gene diversity was observed at DYS385 (0.95) while the lowest was at DYS437 (0.44). A total of 79 different
haplotypes were identified, of which 74 were unique. The haplotype diversity for all loci and discrimination capacity were
calculated as 0.9959 ± 0.0029 and 0.92, respectively. Haplotype data for different neighbouring populations obtained from YChromosome Haplotype Reference Database (YHRD) were used for comparison. The result of the Analysis of Molecular
Variance (AMOVA) indicated that there is no significant genetic distance between Southeastern Anatolia population and
neighbouring populations at all. Armenian, Rasht (Iran-Gilaki) and Izeh (Iran-Bakthiari) populations were found to be closest
to our population, while Syria and Iraq populations were more distant.
INTRODUCTION
Anatolia (Asian part of the present day Turkey) has been occupied by modern humans since
the lower Paleolithic times (Kuhn 2002). It has
acted as a bridge between Balkans and the Near
East for numerous movements of modern humans throughout the history. Anatolia has been
shaped by trade, wars and migrations throughout its history resulting to a very diverse population. Anatolia was populated by various civilizations such as Hattians, the Hurries, the Hittites, the Phrygians, the Lydians, the Urartians,
the Medes, the Romans, the Sassanids, the
Byzantines, the Seljuk Turks and the Ottomans
(Tambets et al. 2000). Southeastern Anatolia
Region is in between Eastern Anatolia and
Mediterranean Regions and has a border with
Syria and Iraq (Fig.1). Southeastern Anatolia
Region is localized in so called “Upper Mesopotamia” which is widely considered as the
cradle of civilization.
Analyzing the distribution of genetic variation within and among populations has long
Address for correspondence:
Dr. F.Ozbas-Gerceker
Associate Professor
Department of Biology
Faculty of Arts & Science
Gaziantep University
Gaziantep, Turkey
Phone: +903423171923;
Fax: +903423229818;
E-mail: [email protected]
been used to gain insight into the demographic
history of humans. Y chromosome, the only
haploid chromosome in the human genome, is
characterized by holoandric transmission and
has a low rate of parallel and recurrent mutations. Thus polymorphisms of Y chromosome
are valuable in reconstruction of paternal lineages thousands and thousands years backwards.
Y-STRs are commonly used to distinguish lineages and to provide information about lineage
relationships (Lowery et al. 2013; Tarlykov et
al. 2013).
Different molecular markers, such as proteins
(Brega et al. 1998), mitochondrial DNA (Mergen et al. 2004; Ottoni et al. 2011) and Y chromosomal markers (Cinnioglu et al. 2004) were
used in the earlier studies to compare Anatolian
population with European and Asian populations. Several studies focusing on Y-STR profiling in Anatolia (Nasidze et al. 2003; Cinnioglu et al. 2004; Rustamov et al. 2004; Donbak
et al. 2006; Alakoc et al. 2010; Serin et al. 2011)
were published previously. Genetic information
on the Southeastern Anatolia Region particularly in relation to Y chromosome-linked markers is scarce. No study for Y-STR profiling of
Southeastern Anatolia population has been carried out yet.
The objective of the present study was to create a Y-STR haplotype database for Southeastern Anatolia population and to explore genetic
relationships of the population with neighbouring populations.
106
FILIZ OZBAS-GERCEKER, NAZLI BOZMAN, AHMET ARSLAN ET AL.
Armenia
TURKEY
Iran
Iraq
Syria
Mediterranean Sea
Diyarbakir
Adiyaman
Gaziantep
Sanliurfa
Siirt
Batman
Sirnak
Mardin
Kilis
Southeastern Anotolia
Fig. 1. Map of the Southeastern Anatolia Region of Turkey
MATERIALS AND METHODS
Study Population
A total of 86 males from the Southeastern
Anatolia region of Turkey were included in this
study. The individuals were paternally unrelated, they had different surnames and they defined themselves as belonging to a paternal lineage residing in the area from at least three generations. Samples were collected in all provinces
of the region; Gaziantep (n=14), Kilis (n=5),
Adiyaman (n=7), Mardin (n=13), Diyarbakir
(n=14), Sanliurfa (n=17), Batman (n=4), Siirt
(n=2) and Sirnak (n=10). Blood samples were
collected using standart procedures in
ethylenediaminetetraacetic acid (EDTA) coated
tubes. The written informed consent was obtained from all participants.
Total genomic deoxyribonucleic acid (DNA)
was isolated from peripheral blood samples by
using a standard salting-out procedure (Miller
et al. 1988). DNA samples were quantified spectrophotometrically and purity was assessed by
electrophoresis in 1% agarose gels and the DNA
was stored at -80 °C.
Genotyping
DNA samples were amplified by using the
commercially available AmpFlSTR Yfiler Polymerase Chain Reaction (PCR) kit (Applied
Biosystems, FosterCity, CA, USA) following the
manufacturer’s recommendations. Y-STR loci
amplified by the kit were; DYS19, DYS385a/b,
DYS389 I/II, DYS390, DYS391, DYS392,
DYS393, DYS390, DYS391, DYS392,
DYS393, DYS437, DYS438, DYS439,
9
10
11
12
13
14
15
16
17
17.2
18
18.2
19
19.2
20
21
22
23
24
25
26
27
28
29
30
31
32
GD1
1
0.151
0.500
0.291
0.047
0.012
0.035
0.570
0.349
0.047
0.012
0.244
0.593
0.151
0.012
0.721
0.023
0.140
0.070
0.023
0.012
0.023
0.535
0.360
0.058
0.023
0.337
0.395
0.128
0.128
0.012
0.012
0.116
0.442
0.372
0.058
0.012
0.140
0.663
0.128
0.058
0.709
0.233
0.058
0.302
0.453
0.186
0.035
0.035
0.151
0.453
0.244
0.116
0.081
0.047
0.395
0.267
0.209
0.058
0.140
0.244
0.209
0.035
0.128
0.070
0.035
0.070
0.012
0.023
0.058
0.430
0.233
0.233
0.047
0.047
0.058
0.407
0.326
0.105
0.058
0.64
0.56
0.71
0.70
0.55
0.45
0.58
0.70
0.65
0.44
0.67
0.52
0.84
0.70
0.72
11, 13
11, 14
11, 15
12, 12
12, 14
12, 15
12, 16
12, 17
12, 18
12, 19
13, 13
13, 14
13, 15
13, 16
13, 17
13, 18
13, 19
14, 13
14, 15
14, 16
14, 17
15, 15
15, 16
15, 17
15, 18
16, 16
16, 17
17, 17
17, 18
0.012
0.128
0.047
0.012
0.023
0.023
0.070
0.047
0.035
0.035
0.023
0.035
0.070
0.035
0.023
0.070
0.023
0.012
0.047
0.012
0.023
0.012
0.012
0.023
0.023
0.012
0.070
0.023
0.023
0.95
Y-STR DATA FOR SOUTHEASTERN ANATOLIA POPULATION
Table 1: Allele frequencies and gene diversities of the 17 Y-STR loci in population sample from Southeastern Anatolia
Allele DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS438 DYS439 DYS437 DYS448 DYS456 DYS458 DYS635 GATAH4 Genotype DYS385
Gene diversity
107
108
0.0749
0.4887
0.9422
0.8586
0.7870
0.2805
0.8458
0.0028
0.0227
0.3110
0.2538
0.1988
0.0657
0.3916
0.3885
0.3902
0.7163
0.0156
0.0882
0.0874
0.0727
0.0153
0.1072
0.2449
0.1409
-0.0049
0.0205
0.6690
0.9821
0.7936
0.9230
0.8905
0.9227
0.0095
-0.0012
-0.0074
p values were shown above and ΦST values below the diagonal. The level of significance is p<0.05.
0.2215
0.8803
0.8715
0.8442
-0.0044
-0.0142
0.0113
-0.0008
-0.0064
0.1665
0.9301
0.8418
-0.0086
-0.0042
-0.0104
0.0176
0.0128
-0.0035
0.3755
0.8072
-0.0064
-0.0108
-0.0013
-0.0097
0.0121
0.0058
-0.0064
0.5345
-0.0065
-0.0064
-0.0097
-0.0115
-0.0131
0.0086
0.0026
-0.0011
-0.0025
0.0000
0.0052
0.0057
-0.0063
-0.0066
0.0091
0.0015
0.0086
Tehran,
Iran
Syria
Rasht,
Iran
Izeh,
Iran
Isfahan,
Iran
Iraq
Azerbaijan
0.6890
0.9674
0.4405
0.5952
0.5353
-0.0148
0.0040
-0.0006
0.0024
*
Seventeen Y-STR loci were genotyped in a
population of Southeastern Anatolia region of
Turkey. A total of 79 different Y-STR haplotypes
were observed in 86 individuals. The majority
of the haplotypes were unique (74/79), while 2
haplotypes were shared by three individuals and
3 were shared by two individuals. The overall
haplotype diversity (HD) was calculated as
Southeastern Anatolia
Armenia
Azerbaijan
Iraq
Isfahan, Iran
Izeh, Iran
Rasht, Iran
Syria
Tehran, Iran
Cukurova, Turkey
RESULTS
Armenia
Arlequin software v.3.5 (Excoffier and
Lischer 2010) was used to calculate allele and
haplotype frequencies, gene diversities (GD) and
haplotype diversity (HD). The discrimination
capacity (DC) was also determined as DC=h/n
where h is the number of different haplotypes
observed in the population (Nei 1987).
Population pairwise genetic distances (RST)
were calculated by using AMOVA with 10.000
permutations using an online tool of the YHRD
and genetic distances were also used to generate Multi-Dimensional Scaling (MDS) plots. For
the population comparison, previously published
haplotype data present in YHRD were used.
Population samples with the number of haplotypes were as follows; Armenian population
(n=100), Azerbaijan population (n=72), Ishafan
Iranian population (n=48) and Tehran, Iranian
population (n=80) (Nasidze et al. 2003), Iraq
Kurds population (n=126) and Syria (Syrian)
population (n=113) (YHRD), Izeh, Iran
(Bakthiari) population (n=50) and Rasht, Iran
(Gilaki) population (n=47) (Roewer et al. 2009),
Cukurova, Turkey population (n=249) (Serin et
al. 2011). Due to the limited data for other populations, analysis was performed on a minimal
European Y-STR haplotype comprising nine
loci: DYS19, DYS389I, DYS389II, DYS385ab,
DYS390, DYS391, DYS392 and DYS393.
Southeastern
Anatolia
Statistical Analysis
Table 2: Pairwise genetic distance matrix based on Φ ST values between Southeastern Anatolia population and neighbouring populations
DYS448, DYS456, DYS458, DYS635/Y GATA
C4 and YGATA H4.
PCR products were separeted by capillary
electrophoresis on an ABI PRISM® 3130 Genetic Analyzer (Applied Biosystems, Foster City,
CA, USA) and typing was done by “Gene Mapper Software v. 3.2” (Applied Biosystems). Allele designations were determined by comparison of the sample fragments with those of allelic ladders provided within the kit.
Cukurova,
Turkey
FILIZ OZBAS-GERCEKER, NAZLI BOZMAN, AHMET ARSLAN ET AL.
109
Y-STR DATA FOR SOUTHEASTERN ANATOLIA POPULATION
0.9959 ± 0.0029 with a discrimination capacity
(DC) of 0.92. The haplotypes were submitted to
the Y-Chromosome Haplotype Reference Database (YHRD) under the accession number
YA003727 and the population was defined as
“Southeastern Anatolia, Turkey [Turkish]”.
The allele frequencies and gene diversity
values of 17 Y-STR loci for the Southeastern
Anatolia population were given in Table 1. Allele frequencies ranged from 0.012 (at more than
one locus) to 0.721 (at DYS392 locus, allele
11) in the population. The highest and the lowest locus gene diversity was observed at DYS385
(0.95) and DYS437 (0.44), respectively. The
average gene diversity value was calculated as
0.65. Intermediate variant alleles (17.2, 18.2 and
19.2) have been found at DYS458 locus with
the second highest GD value (0.84). The frequency of DYS458 variant alleles was % 16.3
in total.
The haplotypes observed in Southeastern
Anatolia population were compared with the
haplotypes of different neighbouring populations
by using data from YHRD database. The
AMOVA pairwise distances based on RST values between populations were calculated and
shown in Table 2.
The genetic distances between the Southeastern Anatolia population and neighbouring populations ranged from -0.0066 to 0.0091, all of
them were found as non-significant (p>0.05).
However, Armenian population and two Iran
populations (Rasht and Izeh) were found to be
much closer than Cukurova (eastern Mediterranean region of Turkey) population which is
the geographically closest neighbour.
MDS plot was also generated by using
pairwise RST values to visualize genetic relationships between population samples (Fig. 2). Armenian, Rasht, Iran (Gilaki) and Izeh, Iran
(Bakthiari) populations were found to be closely
related to our population in both dimensions,
while Syria, Cukurova (Turkey), Isfahan (Iran)
and Iraq populations were much distant.
DISCUSSION
Y-STR profiling has been considered as the
marker of choice for population genetic studies. Previous population genetic studies based
on Y chromosome variations mainly focused on
the general population of Turkey (Cinnioglu et
al. 2004) with only a few samples from the
Southeastern Anatolia region or other different
0.01
0.00
-0.01
Dimension 2
0.02
MDS
Southeastern Anatolia, Turkey
Iraq(Kurds) Armenia (Armenian)
Rasht, Iran (Gilaki) Izeh, Iran (Bakthiari)
Isfahan, Iran (Iranian)
Azarbaijan (Azarbaijani)
Cukurova, Turkey (Turk)
-0.01
0.00
0.01
Dimension 1
stress = 0.0544
Fig. 2. MDS plot based on population pairwise Rst values
Tehran Iran (Iranian)
Syria (Syrian)
0.02
110
FILIZ OZBAS-GERCEKER, NAZLI BOZMAN, AHMET ARSLAN ET AL.
sub-populations such as Cukurova (Serin et al.
2011), Central Anatolia (Alakoc et al. 2010) and
Mediterranean population (Donbak et al. 2006).
This study presents the first population data for
17 Y-STR loci in the Southeastern Anatolia
population.
The Anatolian Peninsula is an important
geographic link between the Middle East, Asia
and Europe. Due to numerous gene flow, admixture and local differentiation processes spanning from the late Pleistocene to the present day,
this region manifests an elaborate genetic constitution (Cavalli-Sforza et al. 1994). Previous
studies suggested that Anatolia had a stepping
stone position between Asian and European
populations and that is closer to the European
populations (Calafell et al. 1996; Comas et al.
1998; Cinnioglu et al. 2004). The Asian genetic
contribution in the Anatolian gene pool has been
attempted to be quantified in many studies.
Cinnioglu et al. (2004) determined the Central
Asian contribution as lower than 9% by comparing the frequencies of Asian specific Y-chromosomal haplogroups C and O3 in Asia and
Anatolia.
Y-STR haplotype analysis revealed a very
high haplotype diversity (0.9959) in Southeastern Anatolia population, similar to populations
from Cukurova (Serin et al. 2011) and Meditterrenaen regions (Donbak et al. 2006) of Turkey.
Due to having experienced many migrations and
hosted various civilizations throughout the history, the Upper Mesopotamia is expected to have
a high haplotype diversity. In concordance with
the results of the previous studies from Turkey,
DYS385 was the most informative marker with
a gene diversity value of 0.95. Intermediate alleles were observed in DYS458 locus in our
population as in the Cukurova population. It has
been reported that these alleles were most frequently found in Northern and the Eastern Africa and Caucasus (Grskovis et al. 2010; Myres
et al. 2007; Ferri et al. 2008) and less common
in Europe (YHRD). These variants occur at low
frequencies but increase the discrimination
power of DNA evidence and therefore become a
useful tool for better understanding regional Y
chromosome variations and recent migrations.
The sample size does not confirm the quality of population sampling in population genetics (Roewer 2003; Willuweit and Roewer 2007).
Having different population specific haplotypes
and resulting high value of haplotype diversity
is the confirmation of sampling quality. However, large sample size provides opportunity to
identify the rare alleles such as variants at
DYS458 locus.
Due to the lack of 17 Y-STR data for several
populations in YHRD, European minimal haplotype set consisting of nine loci with high levels of variability in worldwide populations was
used for AMOVA pair-wise distances based on
RST values between Southeastern Anatolia population and ten neighbouring populations. Nonsignificant values for genetic distances were
obtained between our population and all
neighbouring populations. However, among the
compared populations the closest populations
were Armenian population and two Iran populations (Rasht and Izeh). These populations were
found to be much closer than even another Turkish population from Cukurova (geographically
closest to our population). As the MDS plot
clearly shows, Syria and Iraq (Kurds) populations were also found more distant than others.
But still no significant genetic distance was
found between our population and these populations. Donbak et al. (2006) previously reported
that several Y-STR haplotypes were found to be
shared between Mediterrenean population, Syria
and Iraq populations.
A previous comparative study of Human Leukocyte Antigen (HLA) alleles and haplotypes
in Turkish population revealed that Turks,
Kurds, Armenians, Iranians, Jews, Lebanese and
other Mediterranean groups share a common
ancestry: the older “Mediterranean subsratum”
(Arnaiz-Villena et al. 2001). This might be due
to the fact that Turks, Kurds and Armenians
have been living in the area for many millenia.
Lowery et al. (2013) analyzed the Armenian
population sub-structure by 17 Y-STR loci and
reported that the genetic affinites of the Armenian groups to the Middle East and Anatolia
are greater than to Europe. The present study
also confirmed a close genetic relationship between these populations.
Due to the lack of recombination, Y-STR profiling has the advantage of having greater sensitivity to detect incidents in the demographic
histories of populations. By providing the first
data on Y-STR variations in Southeastern
Anatolia population, this study has an impact
on better understanding of the events contributed to current genetic composition of the population, as well as on male identification in fo-
Y-STR DATA FOR SOUTHEASTERN ANATOLIA POPULATION
rensic crime cases and parentage testing in the
population.
ACKNOWLEDGEMENT
The Authors thank the subjects participated
in this study and Gaziantep University, Scientific Research Projects Governing Unit, for financial support.
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